OPENSEQ.org - YNFA - ECOLI GREMLIN

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YNFA - UPF0060 membrane protein YnfA

UniProt:	P76169	Sequence MIKTTLLFFATALCEIIGCFLPWLWLKRNASIWLLLPAGISLALFVWLLTLHPAASGRVYAAYGGVYVCTALMWLRVVDGVKLTLYDWTGALIALCGMLIIVAGWGRT	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13839
Length:	108 (107)
Sequences:	514
Seq/Len:	4.80

YNFA
Paralog alert: 0.02 [within 20: 0.00] - ratio of genomes with paralogs

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
93_I	100_I	5.483	1.00
76_R	83_L	2.824	1.00
68_V	94_A	2.499	1.00
33_W	36_L	1.704	0.99
46_V	56_S	1.693	0.99
9_F	69_C	1.684	0.99
88_W	92_L	1.625	0.99
20_F	24_L	1.587	0.99
72_L	98_M	1.457	0.98
36_L	40_I	1.422	0.97
21_L	59_V	1.413	0.97
98_M	102_V	1.369	0.97
45_F	67_Y	1.351	0.96
50_T	59_V	1.333	0.96
39_G	43_A	1.322	0.96
7_L	14_C	1.312	0.95
30_A	68_V	1.288	0.95
56_S	79_D	1.26	0.94
51_L	55_A	1.256	0.94
12_A	19_C	1.245	0.93
95_L	99_L	1.234	0.93
50_T	68_V	1.209	0.92
85_L	89_T	1.202	0.92
14_C	41_S	1.19	0.91
85_L	88_W	1.166	0.90
89_T	100_I	1.159	0.90
89_T	93_I	1.151	0.89
73_M	77_V	1.148	0.89
8_F	24_L	1.137	0.89
83_L	105_W	1.134	0.88
7_L	10_A	1.123	0.88
1_M	105_W	1.123	0.88
56_S	67_Y	1.104	0.86
40_I	73_M	1.096	0.86
35_L	39_G	1.091	0.86
60_Y	75_L	1.088	0.85
26_L	62_A	1.082	0.85
17_I	38_A	1.064	0.84
45_F	56_S	1.057	0.83
12_A	70_T	1.052	0.83
19_C	49_L	1.047	0.82
71_A	98_M	1.046	0.82
26_L	50_T	1.042	0.82
92_L	96_C	1.038	0.82
66_V	91_A	1.037	0.81
10_A	96_C	1.034	0.81
8_F	38_A	1.033	0.81
56_S	59_V	1.033	0.81
49_L	67_Y	1.029	0.81
68_V	86_Y	1.028	0.81
25_W	35_L	1.027	0.81
55_A	75_L	1.015	0.79
59_V	79_D	1.013	0.79
27_K	38_A	1.013	0.79
28_R	58_R	1.007	0.79
45_F	75_L	1.005	0.79
94_A	102_V	1.001	0.78

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	P(%)	HHΔ		Acc
2i68A	2	0.9815	95.9	0.858	Contact Map	0.002
3b5dA	2	0.9722	95.1	0.866	Contact Map	0.007
4lepA	2	0.8241	28.8	0.93	Contact Map	0.124
3o7qA	1	1	19.6	0.935	Contact Map	0.104
3wdoA	1	0.8056	19.2	0.936	Contact Map	0.053
4apsA	2	0.8426	18.1	0.936	Contact Map	0.223
2cfqA	1	0.787	12.9	0.94	Contact Map	0.19
4ikvA	1	0.9259	8.3	0.945	Contact Map	0.186
4ldsA	2	0.7593	7.8	0.946	Contact Map	0.191
2gfpA	2	0.8241	6.9	0.947	Contact Map	0.102

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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